I take it that the highlights are in the word document as are the annotations. For best results you need to have a template in the word document that contains the styles you want to work with. Paragraph styles for original text and a different one for annotations and another for headings. However this can be corrected later.

Save as the document as filtered HTML then open up a copy of Sigil. Import the document into Sigil and use Sigil to format the document the way you wish using CSS statements. Word will save some styles at the top of the file. These can be left there are better to move them to a separate CSS, particularly if you decide to break up the single document into multiple files which is easy to do in Sigil. highlights will typically be saved in the file proper with statements like: <span style='background:yellow'>highlighted text</span>

This can be left as is or use a search to replace it with a span reference to an entry in the CSS.

Sigil can use heading styles to automatically create a TOC which will be in a separate file but instantly accessible in various ePub readers. It you also want an inline TOC Sigil can build that also although if you build a TOC in word it will be saved as an inline TOC in the filtered save HTML document.

Sigil also allows you to enter the title, author etc. of the book which it will save inside the book as metadata.

Once you save the Sigil document you will have an ePub eBook for use in various readers.

notes: Highlighting read on monochrome eBook readers can be problematic so you should inspect the results in the reader.

Sigil has its own forum here at MobileRead with lots of help and is a free download.

Dale

Sorry wasn't to clear... I compile new books to read and as I read them on the Nexus I highlight. I will start getting familiar with Sigil and the tips on it's us you gave, thanks.